For GWAS ebi-a-GCST003156, the original summary statistics seem to be defined using the ALT allele as the effect allele. I'll use SNP rs28588851 to illustrate my question, but what I'll ask apply to many SNPs.
In the harmonization, alleles for this SNP were reverse complemented and the beta was multiplied by -1.
This SNP is 1-206202545-G-C in GRCh37, but 1-206138785-C-G in GRCh38, i.e. the alleles are reversed. However, both the original GWAS and harmonization are in GRCh37, so the alleles should be kept as G-C and the beta should be reported for the "C" allele (the original beta).
Please, can someone explain the decision to reverse the sign of beta in this case?
For GWAS ebi-a-GCST003156, the original summary statistics seem to be defined using the ALT allele as the effect allele. I'll use SNP rs28588851 to illustrate my question, but what I'll ask apply to many SNPs.
In the harmonization, alleles for this SNP were reverse complemented and the beta was multiplied by -1.
This SNP is 1-206202545-G-C in GRCh37, but 1-206138785-C-G in GRCh38, i.e. the alleles are reversed. However, both the original GWAS and harmonization are in GRCh37, so the alleles should be kept as G-C and the beta should be reported for the "C" allele (the original beta).
Please, can someone explain the decision to reverse the sign of beta in this case?
Thank you!